Variant report

Variant	rs1876490
Chromosome Location	chr2:73052351-73052352
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:149857730..149860576-chr2:73051525..73053981,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000184678	Chromatin interaction
ENSG00000184270	Chromatin interaction
ENSG00000184260	Chromatin interaction
ENSG00000178096	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10204141	0.82[ASN][1000 genomes]
rs11126381	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11126384	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11686536	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11693376	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11886503	0.90[ASN][1000 genomes]
rs12476137	0.96[CEU][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12479094	0.96[CEU][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12614041	0.90[ASN][1000 genomes]
rs12615163	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12615875	0.90[ASN][1000 genomes]
rs12994646	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13008515	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1396107	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1508060	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1532970	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1876487	0.80[CEU][hapmap]
rs1876489	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2068410	0.85[JPT][hapmap]
rs2135982	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2420882	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35666345	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4597553	1.00[JPT][hapmap]
rs4852891	1.00[YRI][hapmap]
rs4852896	0.92[ASN][1000 genomes]
rs4852900	0.82[ASN][1000 genomes]
rs56181835	0.90[ASN][1000 genomes]
rs56711961	0.90[ASN][1000 genomes]
rs6546787	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6727086	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6744758	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6758539	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6758802	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7577528	0.84[ASN][1000 genomes]
rs7583914	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7586339	0.82[ASN][1000 genomes]
rs7586886	0.92[ASN][1000 genomes]
rs7588400	1.00[YRI][hapmap]
rs7600718	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs970577	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834259	chr2:72941118-73114106	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73051000-73052400	Flanking Active TSS	NHEK	skin
2	chr2:73051200-73052400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr2:73051200-73052600	Flanking Active TSS	Hela-S3	cervix
4	chr2:73051200-73053200	Active TSS	H9 Cell Line	embryonic stem cell
5	chr2:73051400-73052400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr2:73051400-73052400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr2:73051400-73052400	Flanking Active TSS	Fetal Brain Female	brain
8	chr2:73051400-73052600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
9	chr2:73051400-73052600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr2:73051400-73052600	Flanking Active TSS	Adipose Nuclei	Adipose
11	chr2:73051400-73052800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
12	chr2:73051400-73053400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr2:73051400-73053600	Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr2:73051600-73052400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
15	chr2:73051600-73052400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
16	chr2:73051600-73052400	Flanking Active TSS	Brain Hippocampus Middle	brain
17	chr2:73051600-73052400	Flanking Active TSS	Rectal Smooth Muscle	rectum
18	chr2:73051600-73052600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
19	chr2:73051600-73052600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
20	chr2:73051600-73052600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
21	chr2:73051600-73052600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
22	chr2:73051600-73052600	Flanking Active TSS	Duodenum Mucosa	Duodenum
23	chr2:73051600-73052600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
24	chr2:73051600-73052600	Flanking Active TSS	HUVEC	blood vessel
25	chr2:73051600-73053200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr2:73051600-73053200	Active TSS	Placenta	Placenta
27	chr2:73051600-73053400	Active TSS	Colonic Mucosa	Colon
28	chr2:73051600-73053600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:73051800-73052400	Enhancers	Primary B cells from peripheral blood	blood
30	chr2:73051800-73052400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr2:73051800-73052400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
32	chr2:73051800-73052400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
33	chr2:73051800-73052400	Flanking Active TSS	NHLF	lung
34	chr2:73051800-73052400	Flanking Active TSS	Osteobl	bone
35	chr2:73051800-73052600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
36	chr2:73051800-73052600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr2:73051800-73052600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
38	chr2:73051800-73052600	Flanking Active TSS	Dnd41	blood
39	chr2:73051800-73053000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr2:73051800-73053200	Active TSS	Pancreatic Islets	Pancreatic Islet
41	chr2:73051800-73053200	Active TSS	Lung	lung
42	chr2:73051800-73053200	Active TSS	Rectal Mucosa Donor 31	rectum
43	chr2:73051800-73053200	Active TSS	Right Atrium	heart
44	chr2:73051800-73053400	Active TSS	Left Ventricle	heart
45	chr2:73051800-73053600	Active TSS	Esophagus	oesophagus
46	chr2:73052000-73052400	Weak transcription	Small Intestine	intestine
47	chr2:73052000-73052600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr2:73052000-73052600	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
49	chr2:73052000-73052600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr2:73052000-73052600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood

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